Welcome to ipyrad

Documentation

• The ipyrad ethos
• Try it now
• Installation
• Getting Started: Files and Data Types
• Getting Started: Demultiplexing
• Assembly: Parameters
• Assembly: Seven Steps
• Assembly: Branching and Merging
• Assembly: Tutorials
• API: ipyrad assembly workflow
  • Eaton & Ree (2013) single-end RAD data set
  • Demultiplex on i7 outer barcodes
• API: ipyrad analysis tools
  • ipa.vcf_to_hdf5
  • ipa.treemix
  • ipa.pca
  • ipa.raxml
  • ipa.mrbayes
  • ipa.tetrad
  • ipyrad-analysis toolkit: STRUCTURE
  • Cookbook
  • ipa.sratools
  • ipa.baba
  • ipa.bucky
  • ipa.window_extacter
• Frequenty Asked Questions
• Troubleshooting Procedures
• Release Notes

Citation

Eaton DAR & Overcast I. “ipyrad: Interactive assembly and analysis of RADseq datasets.” Bioinformatics (2020).